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Escherichia coli K-12 substr. MG1655 RNA: CyaR small regulatory RNA



Gene: cyaR Accession Numbers: G0-8878 (EcoCyc), b4438, ECK2078

Synonyms: ryeE

Superclasses: a regulatory RNA

Regulation Summary Diagram: ?

Regulation summary diagram for cyaR

Summary:
CyaR is a small RNA that promotes degradation of the ompX [Johansen08, De09], yqaE, nadE, and luxS mRNAs [De09]. Additional targets of CyaR have been identified by comparative genomics [Wright13]. Regulation depends on the presence of Hfq [Johansen08]. Hfq and CyaR interact [Wassarman01], and Hfq may stabilize CyaR [Johansen08].

In an hfq mutant, significantly less CyaR accumulates than in wild type [Moon11]; CyaR is also more unstable in a pnp mutant [De11].

CyaR expression is increased by cAMP-CRP and subject to catabolite repression [Johansen08, De09]. [Johansen08] observed that CyaR expression was upregulated by the alternative sigma factor of the envelope stress response, σE; however, this regulatory effect was not observed by [Guo14].

Ryx: "RNA of unknown function at X position (10 minute) in the genome" [Wassarman01]

CyaR: "cyclic AMP-activated RNA" [Johansen08]

Reviews: [Gottesman01, Hershberg03, Papenfort09, De10, Richards11]

Citations: [Sylwan10]

Map Position: [2,165,138 -> 2,165,224] (46.67 centisomes, 168°)
Length: 87 bp

Genetic Regulation Schematic: ?

Genetic regulation schematic for cyaR

Unification Links: ASAP:ABE-0047258 , EchoBASE:EB4522 , EcoGene:EG31153 , EcoliWiki:b4438 , PortEco:cyaR , RegulonDB:G0-8878

GO Terms:

Biological Process: GO:0070928 - regulation of mRNA stability, ncRNA-mediated Inferred from experiment [De09, Johansen08]
Molecular Function: GO:0000499 - base pairing with mRNA Inferred from experiment [De09]
GO:0005515 - protein binding Inferred from experiment [Wassarman01]
GO:0048027 - mRNA 5'-UTR binding Inferred from experiment [De09]

MultiFun Terms: information transfer RNA related antisense RNA
regulation type of regulation posttranscriptional antisense RNA

Regulated Transcription Units (7 total): ?

Notes:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram

Notes:

History:
Ingrid Keseler on Thu Jul 24, 2008:
Gene start and end positions corrected based on [Johansen08 ].
Suzanne Paley on Thu Oct 21, 2004:
Gene boundaries added from U00096.2 release of genome

Credits:
Last-Curated ? 14-Nov-2013 by Keseler I , SRI International


References

De09: De Lay N, Gottesman S (2009). "The Crp-activated small noncoding regulatory RNA CyaR (RyeE) links nutritional status to group behavior." J Bacteriol 191(2);461-76. PMID: 18978044

De10: De la Cruz MA, Calva E (2010). "The complexities of porin genetic regulation." J Mol Microbiol Biotechnol 18(1);24-36. PMID: 20068355

De11: De Lay N, Gottesman S (2011). "Role of polynucleotide phosphorylase in sRNA function in Escherichia coli." RNA 17(6);1172-89. PMID: 21527671

Gottesman01: Gottesman S, Storz G, Rosenow C, Majdalani N, Repoila F, Wassarman KM (2001). "Small RNA regulators of translation: mechanisms of action and approaches for identifying new small RNAs." Cold Spring Harb Symp Quant Biol 66;353-62. PMID: 12762038

Guo14: Guo MS, Updegrove TB, Gogol EB, Shabalina SA, Gross CA, Storz G (2014). "MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein." Genes Dev 28(14);1620-34. PMID: 25030700

Hershberg03: Hershberg R, Altuvia S, Margalit H (2003). "A survey of small RNA-encoding genes in Escherichia coli." Nucleic Acids Res 31(7);1813-20. PMID: 12654996

Johansen08: Johansen J, Eriksen M, Kallipolitis B, Valentin-Hansen P (2008). "Down-regulation of Outer Membrane Proteins by Noncoding RNAs: Unraveling the cAMP-CRP- and sigma(E)-Dependent CyaR-ompX Regulatory Case." J Mol Biol 383(1):1-9. PMID: 18619465

Moon11: Moon K, Gottesman S (2011). "Competition among Hfq-binding small RNAs in Escherichia coli." Mol Microbiol 82(6);1545-62. PMID: 22040174

Papenfort09: Papenfort K, Vogel J (2009). "Multiple target regulation by small noncoding RNAs rewires gene expression at the post-transcriptional level." Res Microbiol 160(4):278-87. PMID: 19366629

Richards11: Richards GR, Vanderpool CK (2011). "Molecular call and response: the physiology of bacterial small RNAs." Biochim Biophys Acta 1809(10);525-31. PMID: 21843668

Sylwan10: Sylwan L, Frumerie C, Haggard-Ljungquist E (2010). "Identification of bases required for P2 integrase core binding and recombination." Virology 404(2);240-5. PMID: 20627350

Wassarman01: Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S (2001). "Identification of novel small RNAs using comparative genomics and microarrays." Genes Dev 15(13);1637-51. PMID: 11445539

Wright13: Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J (2013). "Comparative genomics boosts target prediction for bacterial small RNAs." Proc Natl Acad Sci U S A 110(37);E3487-96. PMID: 23980183

Other References Related to Gene Regulation

Maciag11: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

Vogt14: Vogt SL, Evans AD, Guest RL, Raivio TL (2014). "The Cpx envelope stress response regulates and is regulated by small noncoding RNAs." J Bacteriol 196(24);4229-38. PMID: 25246476


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Sat Mar 28, 2015, biocyc12.